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I was using RH 6.0, on /dev/sda5, with LILO installed on /dev/sda5 (and /etc/lilo.conf also knew that). I use System Commander on my MBR and winndows on /dev/sda1. When I upgraded to 6.1, by booting from the CD-ROM and choosing the custom upgrade option, the RH setup program installed LILO on my MBR!!! As a result, I couldn't boot my windows partition (/dev/sda1) but Linux booted ok. I had to reinstall System Commander. Then I couldn't boot Linux!!! Maybe because the kernel changed, lilo (the one on /dev/sda5) stopped after saying 'LIL-'. I spent 2 days trying to install lilo again, from a boot disk, because it complained about 'First boot sector does not contain a valid boot sector' whether I tried it on /dev/sda or /dev/sda5. The other day, when I was trying to install it for the last time, before tragically formatting my Linux partition, it installed (with no special options whatsoever). Well, sorry if I wrote too much, but I really got pissed at the RH setup stuff. It REALLY should read /etc/lilo.conf or something to know where lilo is.
Assigned to dledford
This is a bug in the installer, not lilo itself. Reassigning.
This issue was fixed with errata available for 6.1.